Table 1. Phylogenomic data sources: “Human proteins” column refers to the number of genes where the human ortholog was included in the final dataset.

Numbers in brackets refer to the number of human orthologs recovered using our hmmsearch approach (see Methods). Total kept percent after trimming refers to the percent of sites that remained in the final dataset compared to the sum of the lengths of all untrimmed human orthologs.

Dataset name	Genes	Taxa	Sites	Average coverage (by gene)	Average coverage (by site)	Human proteins	Total kept percent after trimming	Reference
Philippe 2009	128	55	30257	82%	73.1%	0 (128)	86.0%	Philippe et al. (2009)
Ryan 2013 EST	406	70	88384	50	41.6	0 (396)	62.5	Ryan et al. (2013)
Whelan 2015 D1	251	76	81006	75	59.6	248	56.6	Whelan et al. (2015)
Borowiec 2015	1080	36	384981	87	75.8	1056	64.7	Borowiec et al. (2015)
Cannon 2016	212	78	44896	80	69.0	212	46.1	Cannon et al. (2016)
Simion 2017	1719	97	401632	74	60.7	1499	40.0	Simion et al. (2017)